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Background Microbial communities associated with indoor dust abound in the built environment. The transmission of sunlight through windows is a key building design consideration, but the effects of light exposure on dust communities remain unclear. We report results of an experiment and computational models designed to assess the effects of light exposure and wavelengths on the structure of the dust microbiome. Specifically, we placed household dust in replicate model “rooms” with windows that transmitted visible, ultraviolet, or no light and measured taxonomic compositions, absolute abundances, and viabilities of the resulting bacterial communities. Results Light exposure per se led to lower abundances of viable bacteria and communities that were compositionally distinct from dark rooms, suggesting preferential inactivation of some microbes over others under daylighting conditions. Differences between communities experiencing visible and ultraviolet light wavelengths were relatively minor, manifesting primarily in abundances of dead human-derived taxa. Daylighting was associated with the loss of a few numerically dominant groups of related microorganisms and apparent increases in the abundances of some rare groups, suggesting that a small number of microorganisms may have exhibited modest population growth under lighting conditions. Although biological processes like population growth on dust could have generated these patterns, we also present an alternate statistical explanation using sampling models from ecology; simulations indicate that artefactual, apparent increases in the abundances of very rare taxa may be a null expectation following the selective inactivation of dominant microorganisms in a community. Conclusions Our experimental and simulation-based results indicate that dust contains living bacterial taxa that can be inactivated following changes in local abiotic conditions and suggest that the bactericidal potential of ordinary window-filtered sunlight may be similar to ultraviolet wavelengths across dosages that are relevant to real buildings. Electronic supplementary material The online version of this article (10.1186/s40168-018-0559-4) contains supplementary material, which is available to authorized users.

Latitudinal gradients are linked to the dynamics of infectious diseases. Both prevalence and infection intensity of the amphibian-killing fungus, Batrachochytrium dendrobatidis (Bd), vary with latitude. Here, we tested whether abiotic and biotic factors are associated with Bd infection prevalence and intensity along a large latitudinal gradient across the Brazilian Atlantic Forest. We detected a positive association between infection prevalence and infection intensity with latitude; elevation, temperature and precipitation best explained infection prevalence, while temperature best explained infection intensity. We also detected a positive association between species richness and Bd infections and associations between Bd infections with host reproductive biology and habitat type. This represents the longest and most thoroughly sampled latitudinal gradient of Bd in anuran populations. Our results corroborate earlier findings that abiotic factors are a major determinant of Bd infections and highlight the need for a better understanding of the role that species diversity plays in disease outcomes.

Antibiotic resistance is increasingly widespread, largely due to human influence. Here, we explore the relationship between antibiotic resistance genes and the antimicrobial chemicals triclosan, triclocarban, and methyl-, ethyl-, propyl-, and butylparaben in the dust microbiome. Dust samples from a mixed-use athletic and educational facility were subjected to microbial and chemical analyses using a combination of 16S rRNA amplicon sequencing, shotgun metagenome sequencing, and liquid chromatography tandem mass spectrometry. The dust resistome was characterized by identifying antibiotic resistance genes annotated in the Comprehensive Antibiotic Resistance Database (CARD) from the metagenomes of each sample using the Short, Better Representative Extract Data set (ShortBRED). The three most highly abundant antibiotic resistance genes were tet(W), blaSRT-1, and erm(B). The complete dust resistome was then compared against the measured concentrations of antimicrobial chemicals, which for triclosan ranged from 0.5 to 1970 ng/g dust. We observed six significant positive associations between the concentration of an antimicrobial chemical and the relative abundance of an antibiotic resistance gene, including one between the ubiquitous antimicrobial triclosan and erm(X), a 23S rRNA methyltransferase implicated in resistance to several antibiotics. This study is the first to look for an association between antibiotic resistance genes and antimicrobial chemicals in dust.

Today there is a wide variety of approaches on how to determine when a river restoration project can be considered ecologically successful. The limited information on river restoration responses renders this practice a subjective component of river management. We aimed to contribute to this issue by assessing the ecological outcomes of a restoration project conducted in Quebrada Chiclana, a first-order tropical stream located in the headwaters of the Rio Piedras in the city of San Juan, Puerto Rico. We focused on the reforestation component of the restoration project using current structure and composition of riparian vegetation as an indicator of restoration success. Recovery of riparian vegetation was studied eight years after restoration using a forest succession approach. We conducted a vegetation census and measured structural variables on vegetation at restored and nearby reference areas. We encountered a riparian vegetation community composed of 35 tree and 84 non-tree species. The non-native trees tall albizia ( Albizia procera ) and African tuliptree ( Spathodea campanulata ) were the most abundant tree species within the study area. We observed 11 out of the 16 woody species initially proposed in the reforestation plan but with lower tree density than proposed. Even though we demonstrate that the river restoration project has not yet met its reforestation objectives, our results show recovery of the vegetation community in the impacted area has occurred through natural succession.

While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.

SUMMARYThe amphibian pathogen Batrachochytrium dendrobatidis (Bd) has recently emerged as a primary factor behind declining global amphibian populations. Much about the basic biology of the pathogen is unknown, however, such as its true ecological niche and life cycle. Here we evaluated invertebrates as infection models by inoculating host species that had previously been suggested to be parasitized in laboratory settings: crayfish (Procambarus alleni) and nematodes (Caenorhabditis elegans). We found neither negative effects on either host nor evidence of persistent infection despite using higher inoculum loads and more pathogen genotypes than tested in previous studies. In contrast, addition of Bd to C. elegans cultures had a slight positive effect on host growth. Bd DNA was detected on the carapace of 2/34 crayfish 7 weeks post-inoculation, suggesting some means of persistence in the mesocosm. These results question the role of invertebrates as alternative hosts of Bd and their ability to modulate disease dynamics.